19-44825957-T-G

Variant names:

• chr19-44825957-T-G
• rs10402271

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.28 in 152,112 control chromosomes in the GnomAD database, including 6,585 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42606 AN: 151994 Hom.: 6578 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42637 AN: 152112 Hom.: 6585 Cov.: 32 AF XY: 0.285 AC XY: 21160 AN XY: 74344

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.286

Alfa AF: 0.320 Hom.: 16830

Bravo AF: 0.279

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10402271; hg19: chr19-45329214;